/*!

\if MANPAGES
\page dcmdjpeg Decode JPEG-compressed DICOM file
\else
\page dcmdjpeg dcmdjpeg: Decode JPEG-compressed DICOM file
\endif

\section dcmdjpeg_synopsis SYNOPSIS

\verbatim
dcmdjpeg [options] dcmfile-in dcmfile-out
\endverbatim

\section dcmdjpeg_description DESCRIPTION

The \b dcmdjpeg utility reads a JPEG-compressed DICOM image (\e dcmfile-in),
decompresses the JPEG data (i. e. conversion to a native DICOM transfer syntax)
and writes the converted image to an output file (\e dcmfile-out).

\section dcmdjpeg_parameters PARAMETERS

\verbatim
dcmfile-in   DICOM input filename to be converted

dcmfile-out  DICOM output filename
\endverbatim

\section dcmdjpeg_options OPTIONS

\subsection dcmdjpeg_general_options general options
\verbatim
  -h    --help
          print this help text and exit

        --version
          print version information and exit

        --arguments
          print expanded command line arguments

  -q    --quiet
          quiet mode, print no warnings and errors

  -v    --verbose
          verbose mode, print processing details

  -d    --debug
          debug mode, print debug information

  -ll   --log-level  [l]evel: string constant
          (fatal, error, warn, info, debug, trace)
          use level l for the logger

  -lc   --log-config  [f]ilename: string
          use config file f for the logger
\endverbatim

\subsection dcmdjpeg_input_options input options

\verbatim
input file format:

  +f    --read-file
          read file format or data set (default)

  +fo   --read-file-only
          read file format only

  -f    --read-dataset
          read data set without file meta information

  # This option allows one to decompress JPEG compressed DICOM objects that
  # have been stored as dataset without meta-header. Such a thing should
  # not exist since the transfer syntax cannot be reliably determined,
  # without meta-header but unfortunately it does.
\endverbatim

\subsection dcmdjpeg_processing_options processing options

\verbatim
color space conversion:

  +cp   --conv-photometric
          convert if YCbCr photometric interpretation (default)

  # If the compressed image uses YBR_FULL or YBR_FULL_422 photometric
  # interpretation, convert to RGB during decompression.

  +cl   --conv-lossy
          convert YCbCr to RGB if lossy JPEG

  # If the compressed image is encoded in lossy JPEG, assume YCbCr
  # color model and convert to RGB.

  +cg   --conv-guess
          convert to RGB if YCbCr is guessed by library

  # If the underlying JPEG library "guesses" the color space of the
  # compressed image to be YCbCr, convert to RGB.

  +cgl  --conv-guess-lossy
          convert to RGB if lossy JPEG and YCbCr is
          guessed by the underlying JPEG library

  # If the compressed image is encoded in lossy JPEG and the underlying
  # JPEG library "guesses" the color space to be YCbCr, convert to RGB.

  +ca   --conv-always
          always convert YCbCr to RGB

  # If the compressed image is a color image, assume YCbCr color model
  # and convert to RGB.

  +cn   --conv-never
          never convert YCbCr to RGB

  # Never convert color space from YCbCr to RGB during decompression.
  # Note that a conversion from YBR_FULL_422 to YBR_FULL will still take
  # place if the source images has been compressed with subsampling.

planar configuration:

  +pa   --planar-auto
          automatically determine planar configuration
          from SOP class and color space (default)

  # If the compressed image is a color image, store in color-by-plane
  # planar configuration if required by the SOP class and photometric
  # interpretation. Hardcopy Color images are always stored color-by-
  # plane, and the revised Ultrasound image objects are stored color-by-
  # plane if the color model is YBR_FULL.  Everything else is stored
  # color-by-pixel.

  +px   --color-by-pixel
          always store color-by-pixel

  # If the compressed image is a color image, store in color-by-pixel
  # planar configuration.

  +pl   --color-by-plane
          always store color-by-plane

  # If the compressed image is a color image, store in color-by-plane
  # planar configuration.

SOP Instance UID:

  +ud   --uid-default
          keep same SOP Instance UID (default)

  #  Never assigns a new SOP instance UID.

  +ua   --uid-always
          always assign new UID

  # Always assigns a new SOP instance UID.

workaround options for incorrect JPEG encodings:

  +w6   --workaround-pred6
          enable workaround for JPEG lossless images
          with overflow in predictor 6

  # DICOM images with 16 bits/pixel have been observed "in the wild"
  # that are compressed with lossless JPEG and need special handling
  # because the encoder produced an 16-bit integer overflow in predictor
  # 6, which needs to be compensated (reproduced) during decompression.
  # This flag enables a correct decompression of such faulty images, but
  # at the same time will cause an incorrect decompression of correctly
  # compressed images. Use with care.

  +wi   --workaround-incpl
          enable workaround for incomplete JPEG data

  # This option causes dcmjpeg to ignore incomplete JPEG data
  # at the end of a compressed fragment and to start decompressing
  # the next frame from the next fragment (if any). This permits
  # images with incomplete JPEG data to be decoded.

  +wc   --workaround-cornell
          enable workaround for 16-bit JPEG lossless
          Cornell images with Huffman table overflow

  # One of the first open-source implementations of lossless JPEG
  # compression, the "Cornell" library, has a well-known bug that leads
  # to invalid values in the Huffmann table when images with 16 bit/sample
  # are compressed. This flag enables a workaround that permits such
  # images to be decoded correctly.

\endverbatim

\subsection dcmdjpeg_output_options output options

\verbatim
output file format:

  +F    --write-file
          write file format (default)

  -F    --write-dataset
          write data set without file meta information

output transfer syntax:

  +te   --write-xfer-little
          write with explicit VR little endian (default)

  +tb   --write-xfer-big
          write with explicit VR big endian TS

  +ti   --write-xfer-implicit
          write with implicit VR little endian TS

post-1993 value representations:

  +u    --enable-new-vr
          enable support for new VRs (UN/UT) (default)

  -u    --disable-new-vr
          disable support for new VRs, convert to OB

group length encoding:

  +g=   --group-length-recalc
          recalculate group lengths if present (default)

  +g    --group-length-create
          always write with group length elements

  -g    --group-length-remove
          always write without group length elements

length encoding in sequences and items:

  +e    --length-explicit
          write with explicit lengths (default)

  -e    --length-undefined
          write with undefined lengths

data set trailing padding (not with --write-dataset):

  -p=   --padding-retain
          do not change padding (default if not --write-dataset)

  -p    --padding-off
          no padding (implicit if --write-dataset)

  +p    --padding-create  [f]ile-pad [i]tem-pad: integer
          align file on multiple of f bytes
          and items on multiple of i bytes
\endverbatim

\section dcmdjpeg_transfer_syntaxes TRANSFER SYNTAXES

\b dcmdjpeg supports the following transfer syntaxes for input
(\e dcmfile-in):

\verbatim
LittleEndianImplicitTransferSyntax             1.2.840.10008.1.2
LittleEndianExplicitTransferSyntax             1.2.840.10008.1.2.1
DeflatedExplicitVRLittleEndianTransferSyntax   1.2.840.10008.1.2.1.99 (*)
BigEndianExplicitTransferSyntax                1.2.840.10008.1.2.2
JPEGProcess1TransferSyntax                     1.2.840.10008.1.2.4.50
JPEGProcess2_4TransferSyntax                   1.2.840.10008.1.2.4.51
JPEGProcess6_8TransferSyntax                   1.2.840.10008.1.2.4.53
JPEGProcess10_12TransferSyntax                 1.2.840.10008.1.2.4.55
JPEGProcess14TransferSyntax                    1.2.840.10008.1.2.4.57
JPEGProcess14SV1TransferSyntax                 1.2.840.10008.1.2.4.70
\endverbatim

(*) if compiled with zlib support enabled

\b dcmdjpeg supports the following transfer syntaxes for output
(\e dcmfile-out):

\verbatim
LittleEndianImplicitTransferSyntax             1.2.840.10008.1.2
LittleEndianExplicitTransferSyntax             1.2.840.10008.1.2.1
BigEndianExplicitTransferSyntax                1.2.840.10008.1.2.2
\endverbatim

\section dcmdjpeg_logging LOGGING

The level of logging output of the various command line tools and underlying
libraries can be specified by the user.  By default, only errors and warnings
are written to the standard error stream.  Using option \e --verbose also
informational messages like processing details are reported.  Option
\e --debug can be used to get more details on the internal activity, e.g. for
debugging purposes.  Other logging levels can be selected using option
\e --log-level.  In \e --quiet mode only fatal errors are reported.  In such
very severe error events, the application will usually terminate.  For more
details on the different logging levels, see documentation of module "oflog".

In case the logging output should be written to file (optionally with logfile
rotation), to syslog (Unix) or the event log (Windows) option \e --log-config
can be used.  This configuration file also allows for directing only certain
messages to a particular output stream and for filtering certain messages
based on the module or application where they are generated.  An example
configuration file is provided in <em>\<etcdir\>/logger.cfg</em>.

\section dcmdjpeg_command_line COMMAND LINE

All command line tools use the following notation for parameters: square
brackets enclose optional values (0-1), three trailing dots indicate that
multiple values are allowed (1-n), a combination of both means 0 to n values.

Command line options are distinguished from parameters by a leading '+' or '-'
sign, respectively.  Usually, order and position of command line options are
arbitrary (i.e. they can appear anywhere).  However, if options are mutually
exclusive the rightmost appearance is used.  This behavior conforms to the
standard evaluation rules of common Unix shells.

In addition, one or more command files can be specified using an '@' sign as a
prefix to the filename (e.g. <em>\@command.txt</em>).  Such a command argument
is replaced by the content of the corresponding text file (multiple
whitespaces are treated as a single separator unless they appear between two
quotation marks) prior to any further evaluation.  Please note that a command
file cannot contain another command file.  This simple but effective approach
allows one to summarize common combinations of options/parameters and avoids
longish and confusing command lines (an example is provided in file
<em>\<datadir\>/dumppat.txt</em>).

\section dcmdjpeg_environment ENVIRONMENT

The \b dcmdjpeg utility will attempt to load DICOM data dictionaries specified
in the \e DCMDICTPATH environment variable.  By default, i.e. if the
\e DCMDICTPATH environment variable is not set, the file
<em>\<datadir\>/dicom.dic</em> will be loaded unless the dictionary is built
into the application (default for Windows).

The default behavior should be preferred and the \e DCMDICTPATH environment
variable only used when alternative data dictionaries are required.  The
\e DCMDICTPATH environment variable has the same format as the Unix shell
\e PATH variable in that a colon (":") separates entries.  On Windows systems,
a semicolon (";") is used as a separator.  The data dictionary code will
attempt to load each file specified in the \e DCMDICTPATH environment variable.
It is an error if no data dictionary can be loaded.

\section dcmdjpeg_see_also SEE ALSO

<b>dcmcjpeg</b>(1)

\section dcmdjpeg_copyright COPYRIGHT

Copyright (C) 2001-2019 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.

*/
